Hi Li, My previous answer will not just give you all genes, but all the isoforms as well, and that's probably not what you wanted. To get just genes use the knownCanonical table and click the "describe table schema" button.
knownCanonical is linked to knownGene: hg19.knownGene <http://hgwdev.cse.ucsc.edu/cgi-bin/hgTables?hgsid=3432404&hgta_doSchemaDb=hg19&hgta_doSchemaTable=knownGene>.name (via knownCanonical.transcript), and is just the genes, without the isoforms. Please let us know if you have any additional questions: [email protected] - Greg Roe UCSC Genome Bioinformatics Group On 1/9/12 11:39 AM, Greg Roe wrote: > Hi Li, > > If you go to the table browser (http://genome.ucsc.edu/cgi-bin/hgTables) > select the knownGene table and click the "describe table schema" it will > show you how many records (genes) are in the table. There are no > duplicates in this table: > > mysql> SELECT name, COUNT(*) AS Count > -> FROM knownGene > -> GROUP BY name > -> HAVING Count> 1; > Empty set (0.03 sec) > > Keep in mind that this is not necessarily the complete set of genes in > humans. UCSC Genes is a fairly conservative set of "known" genes. Other > gene sets may contain greater or fewer numbers of genes. > > Please let us know if you have any additional questions: [email protected] > > - > Greg Roe > UCSC Genome Bioinformatics Group > > > > On 1/7/12 1:24 AM, yuanf li wrote: >> Dear Project: >> I just want to know how many genes are in UCSC known gene database? Removing >> duplications? Thank you! >> >> Li Yuanfeng >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
